Auto optical isomer ex symmetry arkane #1571
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@goldmanm, many of Arkane's tests still use the |
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@alongd, fixes for the tests should be back up. I was trying to fix a codacy issue and ended up pushing outdated version of the branch. force pushing is dangerous. |
arkane/log.py
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| symmetry = pg.symmetryNumber | ||
| logging.debug("Symmetry algorithm found {0} optical isomers and a symmetry number of {1}".format(optical_isomers,symmetry)) | ||
| else: | ||
| logging.warning("Symmetry algorithm errored when computing optical isomers. Setting to 1") |
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I think this should be a logging.error level, and the text should tell the user to try re-running and supply the missing values (unless we want to raise an error?)
Also, the current message only refers to opt isomers, symmetry could be problematic as well
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I wonder how making this an error might cause issues when integrating with ARC (or other automated software generation). I guess we just have to integrate the code in a way such that a factor of two error does not destroy the whole RMG run.
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Changed to logging.error
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@goldmanm, let's rebase and merge this PR, then do the respective ARC PR |
This commit makes the Log file readers for QChem, Gaussian and Molepro inherit from the base Log class, which can reduce code duplication going forward. To do this, the method `determine_qm_software` was removed from the Log class as this causes circular import errors, and the `Log` class was moved to a separate file, in accordance with PEP-8. Methods used in all child classes are added to the parent Log class. This commit also modified methods calling `determine_qm_software`, and references to `isinstance(x,Log)` were altered to not include the children log files.
Previously, not having the number of opticalIsomers would throw and error. Now the computer can estimate the number of optical isomers, so no input is accepted.
Prevously loadConformer required an integer input for optical isomers. This commit allows this method to call the Symmetry package and estimate the value automatically.
Created new method get_optical_isomers_and_symmetry_number in Log class This method allows Log objects to calculate the number of optical isomers and symmetry numbers contained within a log file. This was taken and modified from the equivalent method in ARC (credits to Alon). Remove symfromlog parameter. If using the RMG QM symmetry package, the symfromlog parameter is not necessary and confusing. This commit removes the need for such a parameter. Get Arkane to use Symmetry package for symmetry. This commit uses the Symmetry package to estimate symmetry if not explicitly given by the user by modifying the gaussian, molpro, and qchem parsers.
Previously, no error was raised when the `linear` parameter was not implemented properly. This could hide information about incorrect calculations if the user is not properly implementing the parameter. This commit raises an error if no `linear` parameter is given.
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Motivation or Problem
Currently Arkane requires optical isomer input.
Description of Changes
This PR allows Arkane to estimate optical isomer and symmetry using the qm symmetry package.
Testing
symfromlogboolean was removed.Reviewer Tips
Run an arkane calculation with & without the symmetry and optical isomer parameter.